Genome.

Assay objective: To co-capture viral integration sites and intact-proviral-genomes from single templates. See Einkauf et al.

1️⃣ Approach

🅰️ Primers

Second round MipSeq Primers
HIV-1 HXB2 Start and End Coordinates and Regions
Primer Sequence Start End Gene gene_start gene_stop direction
1
2.5 5'-CCTAGGAAAAAGGGCTGTTGGAAATGTGG-3' 2,011 2,039 gag 1222 1250 fw
RT3789R 5'-CAAACTCCCACTCAGGAATCCA-3' 3,777 3,798 pol 1693 1714 rc
2
U5-638F GCGCCCGAACAGGGACYTGAAARCGAAAG 638 666 NCR (downstream 5LTR) NA NA fw
ProC- GAGTATTGTATGGATTTTCAGGCCCAAT 2,724 2,967 pol (RT) 613 (148) 640 (175) rc
3
VP5549F AGAGGATAGATGGAACAAGCCCCAG 5,550 5,574 Vif (vpr) 510 (1) 534 (16) fw
V3CR TGCTCTTTTTTCTCTCTSCACCACT 7,736 7,760 gp160 (gp120) 1512 (1512) 1536 (1533) rc
4
GP41Fi GGACAATTGGAGAAGTGAATTAT 7,652 7,674 gp160 (gp120) 1428 (1428) 1450 (1450) fw
U5-547R GCACTCAAGGCAAGCTTTATTGAGGCTTA 9,604 9,632 LTR3 (LTR5) 519 547 rc
5
RT3626F TGCCCACACTAATGATGTAA 3,626 3,645 pol (RT) 1542 (1077) 1561 (1096) fw
SC02R CTTCCTGCCATAGGAGATGCCTA 5,980 5,958 Tat1 (Rev1) 128 (1) 150 (11) rc

🅱️ Amplicons

2️⃣ Pool Processing WGS

📊 Purity

Bar plot of minor SNP frequencies across SGS amplicons. The expected consensus base (100%) is excluded. Each colored bar indicates the relative frequency of a minor allele at a given position. Low frequencies (<1–2%) are consistent with sequencing error, whereas higher prevalence of higher peaks may suggest contamination or multiple templates (insufficient dilution?).

Sample MDA-04

1

Sample MDA-05

1

Sample MDA-06

1

📊 Coverage

Coverage of SGS amplicons across nucleotide positions. The y-axis shows the sequencing depth at each position on a log₁₀ scale. Bars indicate the number of reads supporting each base, with colors corresponding to the primer set used for amplification (faceted by primer). Uniform high coverage across the amplicon indicates reliable sequencing, while dips or gaps suggest regions of poor amplification or sequencing dropout.

Sample MDA-04

Sample MDA-05

Sample MDA-06